The pattern of carbon (C) allocation among the different pools is an important ecosystem structural feature, which can be modified as a result of changes in environmental conditions that can occur gradually (e.g., climatic change) or abruptly (e.g., management practices). This study quantified the C pools of plant biomass, litter and soil in an arid shrubland in Chile, comparing the natural condition (moderately disturbed by grazing) vs. the afforested condition (two-year-old plantation with Acacia saligna (Labill.) H.L. Wendl.), each represented by a 60 ha plot. To estimate plant biomass, allometric functions were constructed for the four dominant woody species, based on the volume according to their shape, which showed high correlation (R2 > 0.73). The soil was the largest C pool in both natural and afforested conditions (89% and 94%, respectively) and was significantly lower in the afforested than natural condition at all five soil depths. The natural condition had in total 36.5 ton (t) C ha−1 compared to 21.1 t C ha−1 in the afforested condition, mainly due to C loss during soil preparation, prior to plantation of A. saligna. These measurements serve as an important baseline to assess long-term effects of afforestation on ecosystem C pools.